Virgo Benchmarking Datasets

1. Global Ocean Eukaryotic Viral (GOEV) DatabaseSource: Extract from Gaïa M. et al. Nature (2023)Components:591 MAGs from Schulz, F. et al. (2020) [DOI: 10.1038/s41586-020-1957-x]445 MAGs from Sunagawa, S. et al. (2020) [DOI: 10.1038/s41579-020-0364-5]218 MAGs from Moniruzzaman, M. et al. (2020) [DOI: 10.1038/s41467-020-15507-2]158 reference viral assembliesAccessed: July 20, 2024Data File: GOEV_DB_CONTIGS.db.zip from FigshareSelection Criteria: Only contigs labeled at the Order taxonomic level were retainedSampling Method: Not applicableFinal Sample Size: 1,412 viral contigs--2. Known Viral Sequence Clusters (kVSCs)Source: Extract from Zolfo, M. et al. (2024) [DOI: 10.1101/2024.02.19.580813]Data Files:VSC5_rep_fnas_nr99_45k_metaphlanDB.fna.gzVSCs_groups.csv metadataDownloaded From: Zenodo, last accessed June 28, 2024Selection Criteria:Started from 45,872 representative sequences from MetaPhlan 4.1Selected kVSCs (sequences clustering with a RefSeq representative)Verified RefSeq accessions against ICTV Release #39 for accurate labelingSampling Method: RefSeq matching based on metadataFinal Sample Size: 2,232 representative sequences--3. ICTV Release #39Source: International Committee on Taxonomy of Viruses (ICTV) Release #39Downloaded Using: ICTVdump tool on July 17, 2024Selection Criteria:Viruses present in both VMR releases #37 and #39At least two representatives per familySampling Method: Up to 5 genomes randomly sampled per family using pandas.sample(), 192 families represented.Final Sample Size: 860.--4. RefSeq Viral Dataset (Random Iteration)Source: NCBI Virus Portal NCBI Virus accessed on January 27, 2025Selection Criteria:Viruses with an assigned family-level taxonomy, up to 43 viruses per familySampling Method: Random uniform samplingFinal Sample Size: 6,778 viral genomes--5. RefSeq Viral Dataset (Prokaryote-Infecting)Source: NCBI Virus Portal NCBI Virus accessed on January 27, 2025Selection Criteria:Viruses with an assigned family-level taxonomyProkaryote-infecting viruses onlySampling Method: Random uniform samplingFinal Sample Size: 3,536 viral genomes--6. ICTV Release #39 (Reduction Study Subset)Source: International Committee on Taxonomy of Viruses (ICTV) Release #39Downloaded Using: ICTVdump tool on July 17, 2024Selection Criteria: 1,000 viruses randomly sampled from the full releaseSampling Method: Random uniform samplingFinal Sample Size: 1,000 viral genomesNotes: Reduction study starting data. We provide the source code for generating the fragmented genomes.